Traditional evaluation of DNA methylation in fish using invasive tissue biopsy limits its application for in vivo monitoring and genetic selection for resistant individuals. As a non-invasive approach, plasma circulating cell-free DNA (cfDNA) testing has become a prospective strategy for studying individual epigenetic states and immune responses recently. In this study, the genome-wide methylation profiles in cfDNA by whole-genome bisulfite sequencing (WGBS) were evaluated for the GIFT strain of Nile tilapia (Oreochromis niloticus) following Streptococcus agalactiae infection. The cfDNA concentration in the susceptible group (2.72 ± 1.46 ng/μL) was significantly higher than that in the control (1.12 ± 0.38 ng/μL) and resistant group (1.23 ± 0.72 ng/μL). A total of 3076 differentially methylated regions (DMRs) were identified between resistant and susceptible groups, and the DMR-associated genes were significantly enriched in pathways related to transcriptional regulation, immune response, and energy metabolism. By integrating published spleen methylation data and conducting RNA-seq in spleen, we further explored the potential tissue origin of cfDNA methylation markers. Approximately 7.6% of cfDNA DMRs (234) overlapped with the spleen DMRs, and 111 overlapping DMRs with consistent methylation direction showed a strong correlation between the cfDNA and spleen datasets (R = 0.928, p < 1.31e - 48). Promoter methylation levels in cfDNA were negatively correlated with gene expression in spleen transcriptome data. 100 differentially expressed genes (DEGs) that were detected in spleen data were also observed in the cfDNA gene dataset with differentially methylated promoters (DMPs). BS-PCR and qRT-PCR analyses confirmed significant differences in methylation and expression of candidate genes b4galt1l, pigr and adsl across four immune-related tissues (spleen, head kidney, liver, and hindgut) between the control and infected groups. In summary, this study provides a valuable epigenetic dataset for developing epigenetic biomarkers in GIFT tilapia breeding for resistance to S. agalactiae and indicates that spleen could be one of the potential tissue sources of cfDNA methylation marks.

Global food security is increasingly constrained by population growth, resource limitations, and climate change, while capture fisheries have reached or exceeded sustainable production limits. Aquaculture has expanded rapidly to fill this gap, yet persistent concerns remain regarding its environmental, social, and economic sustainability. This review synthesizes evidence from 1990 to 2026 using a combined systematic and narrative approach to evaluate key sustainability challenges and the effectiveness of existing and emerging solutions. Evidence indicates that established interventions can substantially mitigate environmental impacts: recirculating aquaculture systems significantly reduce water use and nutrient discharge, integrated multi-trophic aquaculture enhances nutrient recovery, and advances in vaccination and selective breeding improve disease resistance. However, adoption remains uneven due to high capital costs, regulatory constraints, and limited accessibility for small-scale producers. Emerging technologies, including artificial intelligence, genome editing, and digital traceability, offer further potential to improve efficiency and sustainability, although challenges related to scalability, governance, and social acceptance persist. We propose a “precision sustainability” framework that integrates technological innovation, adaptive management, and inclusive governance to support context-specific solutions. This framework provides a structured pathway to align aquaculture development with environmental protection and social equity, strengthening its role in sustainable global food systems.

Pogostemon cablin (Blanco) Benth. (patchouli) is a commercially valuable spice and medicinal herb, highly valued for its essential oil rich in sesquiterpenoids, with patchoulol as the key component dictating its aromatic and therapeutic properties. With the surging global demand for natural patchoulol, targeted metabolic engineering to enhance the yield and quality of P. cablin is urgently required. MYC transcription factors (TFs) play crucial roles in regulating plant secondary metabolism, but their role in modulating sesquiterpene biosynthesis in P. cablin remains unclear. Here, we characterized PatMYC1, a jasmonic acid (JA)-responsive bHLH/MYC TF in P. cablin. As a transcriptional activator, PatMYC1 specifically binds to G-box cis-elements in the promoters of PatHMGR and PatGPPS to activate their transcription. Transient overexpression of PatMYC1 markedly upregulates six key genes of the cytoplasmic mevalonate (MVA) pathway and elevates sesquiterpenoid content, whereas VIGS-based gene knockdown causes repressed gene expression and reduced metabolite accumulation. Importantly, PatMYC1 directly targets only PatHMGR and PatGPPS, while transcriptional changes in the other four MVA pathway genes (PatHMGS, PatPMK, PatMDD, and PatFPPS) result from indirect regulatory cascades. Collectively, PatMYC1 serves as a positive transcriptional regulator of patchouli sesquiterpene biosynthesis, selectively activating two direct target genes within the MVA pathway. This study provides a potential gene resource for future patchouli metabolic engineering and advances our understanding of JA-dependent terpenoid regulatory networks in medicinal aromatic plants.

Fish osmoregulation was characterized by modifications in both the structure and functionality of numerous osmoregulatory cells and organs. Single-cell resolution investigations are imperative for comprehending the cellular processes involved in salinity-induced stress in fish. In this study, a cell atlas of the kidney of Genetically Improved Farmed Tilapia (GIFT) exposed to 27 ​ppt high-salinity stress for one month was established using scRNA-seq. We first identified 16 principal cell clusters, including podocytes (PODs), vascular endothelial cells (VasEndo), T cells, parietal epithelial cells (PECs), renal interstitial cells (RICs), vascular smooth muscle cells (SMCs), distal early tubule (DE), proximal convoluted tubule (PCT), B cells, hematopoietic stem/progenitor cells (HSPCs), macrophages/dendritic cells (MΦ/DCs), renal progenitor cells (RPCs), juxtaglomerular apparatus (JGA), proximal straight tubule (PST), and multiciliated cells (MCCs). A notable augmentation in the gene expression and proportions of PECs was observed, underscoring their pivotal function in the adaptive response of the kidney to high salinity stress. Analysis of RNA velocity unveiled a transitional connection between PECs and PODs, suggesting that PECs might act as precursor cells for PODs. Particularly, mature podocytes (MP) displayed resilience in high-salinity conditions, with kirrel1b, situated at the QTL region LG18: 26,733,536–26,809,639, pinpointed as a distinguishing novel gene marker for MP and a potential candidate gene for salinity endurance. Interestingly, the high-salinity levels substantially suppressed the expression of genes linked to lipid metabolism, such as plin2, srebf2, and dgat1, in renal tubular epithelial cells (PCT, PST, and DE), indicating a decline in lipid droplet formation and lipid synthesis. These discoveries provided valuable perspectives into the cellular and molecular mechanisms involved in salinity adaptation in tilapia.

The orange-spotted grouper (Epinephelus coioides) is an economically important marine species in the South China Sea. Due to overfishing and environmental pollution, its natural resources in the South China Sea have severely declined. Evaluation of genetic diversity of the orange-spotted grouper in the distribution areas is important for future conservation action. In this study, a molecular marker specific for orange-spotted grouper E. coioides was developed based on the mitochondrial D-loop region sequences. We evaluated the community structure and genetic diversity of the groupers at four stock enhancement sites of the Wanshan Archipelago by employing integrated assessment methods including environmental DNA (eDNA) and the D-loop marker. Five grouper species were identified from the eDNA samples using 12S rDNA metabarcoding technology, with the orange-spotted grouper being the most abundant grouper ranging from 39.05% to 49.79% of the grouper contents. Furthermore, 15 D-loop haplotypes for the orange-spotted grouper in the Wanshan Archipelago release areas were detected by utilizing the novel developed D-loop marker. High haplotype genetic diversity was observed at all sampling sites for the orange-spotted grouper population. Dominant haplotypes such as ASV_1, ASV_2, ASV_3, ASV_4, and ASV_5 exhibited high levels of geographic sharing, suggesting a degree of ecological or environmental similarity across these regions. Most of the genetic variations were originated within populations, indicating significant genetic differentiation among grouper populations in the Wanshan Archipelago. Our study indicates that eDNA technology is a valuable non-invasive tool for monitoring fish community structure, and the haplotype diversity of E. coioides in the sampled waters maintained a relatively high haplotype richness.

Culturing saline tilapia has become a new trend in the aquaculture due to the scarcity of freshwater resources. In this study, the genetic basis controlling for salt tolerance were investigated by using a ddRAD-seq-based GWAS in 288 individuals with extreme salt tolerant traits from half-sib families of red tilapia. 12 genome-wide significant SNPs and 6 chromosome-wide significant SNPs associated with acute salt tolerance were identified. Two QTLs on LG18:25,593,701–7009020 and on LG16:19,735,164–21,231,391 were defined. It is noteworthy that the QTL on LG16 is a novel QTL associated with acute salt stress. Near the significant SNP sites, we identified candidate genes sik1, ltb4r2b, pnp5b and kirrel1b with differential transcript expression under salt stress. Furthermore, significant physiological differences in serum osmolality and ion concentrations were confirmed between the tolerant group and sensitive group under 4.5 h of 22 ppt stress. The sensitive group had much higher serum osmolality (osmolality: 642.20 ± 6.30 mOsm/kg) and higher concentrations of sodium and chloride ions (sodium: 317.67 ± 5.03 mmol/L and chloride: 316.43 ± 8.28 mmol/L) than the tolerant group (547.60 ± 15.44 mOsm/kg, p osmolality = 0.0002; sodium: 280.53 ± 9.13 mmol/L, p sodium < 0.0242; chloride: 266.00 ± 12.00 mmol/L, p chloride < 0.0184). However, the lowest bicarbonate concentration was detected in the sensitive group at 22 ppt (2.53 ± 0.30 mmol/L), which was significantly different from both the sensitive group at 0 ppt (p = 0.0008) and the tolerant group at 22 ppt (p = 0.0164). Our research laid the foundation for exploring the genetic mechanisms of acute salt tolerance and osmoregulation in red tilapia and for developing strains of red tilapia adapted to saltwater.

Long noncoding RNAs (lncRNAs) are increasingly recognized as key players in various biological processes, yet their role in fish's response to salinity changes remains largely unexplored. This study undertakes a genome-wide analysis of lncRNAs in Nile tilapia (Oreochromis niloticus), examining their response to salinity stress across a substantial dataset of 98 RNA-seq samples from nine different tissues. We identified 28,819 high-confidence lncRNA candidates, which are characterized by a shorter average length of 788 nucleotides and fewer exons (average 1.84) compared to mRNAs. Specifically, in the gills exposed to salinity 27 for three and a half months, we found 846 differentially expressed lncRNAs (DElncRNAs), including 342 upregulated and 504 downregulated transcripts. The study also highlighted 220 significant DElncRNA-mRNA pairs, indicating potential regulatory interactions. Notably, in response to acute salinity stress, we identified 989 DElncRNAs, with 414 upregulated and 575 downregulated in gills. An analysis of these DElncRNAs revealed 348 high-confidence pairs, with Gene Ontology (GO) and KEGG pathway analyses indicating a prominent role in immune-inflammatory responses for most target genes, such as trim7, trim35, trim47, cd225. Crucially, two DElncRNAs (ENSONIT00000076723 and MSTRG.18195.2) were found to co-localize with QTL intervals associated with salinity tolerance, situated near three significant SNPs. Additionally, a notable cis-acting pair, consisting of mRNA ENSONIT00000087370 (apold1a) and lncRNA ENSONIT00000076723, demonstrated a strong correlation under both acute and chronic hypo-osmotic stress. Our findings significantly broaden the understanding of lncRNAs in salinity stress adaptation and suggest their novel roles as key regulators in the osmoregulatory mechanisms of Nile tilapia.

This study investigated the effects of dietary supplementation with Litsea cubeba essential oil (LEO) on growth performance, immune function, intestinal health, and microbiota composition in channel catfish (Ictalurus punctatus). An eight-week feeding trial was conducted with 750 fish (60.00 ± 0.50 g) assigned to five diets: 0 (CON), 100 mg/kg (LEO100), 200 mg/kg (LEO200), 400 mg/kg (LEO400), and 800 mg/kg (LEO800). The LEO100 and LEO200 groups showed significant improvements in growth performance, immune response (C3, C4, and ACP levels), and digestive enzyme activities (amylase, lipase, and trypsin). Gene expression analysis revealed an upregulation of genes related to intestinal barrier integrity (zo-1, zo-2, and occludin), immunoregulatory cytokines (tgf-β1, tgf-β2, tgf-β3, and il-10), and key transcriptional regulators nf-κb and stat3). Conversely, pro-inflammatory mediators (il-8, il-1β, and tlr5) were significantly downregulated. In the LEO100 and LEO200 groups, the protein expression of TNF-α and NF-κB was elevated. Additionally, intestinal morphology (villus height, muscle thickness, and goblet cell count) and beneficial microbiota (Lactococcus and Plesiomonas) were enhanced in the LEO100 and LEO200 groups. These results demonstrate that dietary supplementation with LEO at 100-200 mg/kg improves growth performance, immune function, and intestinal health in channel catfish, making it a promising natural feed additive for aquaculture.

This study evaluated the effects of ginseng polysaccharide (GP) supplementation on the growth performance, immunity, intestinal microbiota, and antibacterial activity of channel catfish (Ictalurus punctatus). Over a 56-day feeding trial, 750 catfish (60.03 ± 0.5 g) were fed diets containing GP at five concentrations: 0 mg/kg (CON), 200 mg/kg (GP200), 400 mg/kg (GP400), 800 mg/kg (GP800), and 1600 mg/kg (GP1600). GP supplementation at 200-800 mg/kg significantly enhanced growth performance, digestive enzyme activities (amylase, lipase, and trypsin), and reduced the feed conversion ratio (P < 0.05). The treatment significantly enhanced transcriptional activation of epithelial barrier-associated genes (zo-1, zo-2, and occludin), upregulated immunoregulatory mediators (tgf-β1, tgf-β2, tgf-β3, and il-10), and modulated key immune signaling pathways (tlrs, nf-κb, and Nrf2-keap1), Conversely, it suppressed pro-inflammatory signaling molecules (il-1β, il-8, tnf-α, and nf-κb) (P < 0.05). Additionally, GP supplementation improved intestinal histology (villus height, muscular thickness, and goblet cell numbers) and enriched beneficial gut microbiota, particularly Lactococcus and Weissella. Metabolic pathways related to phenylalanine metabolism and fatty acid degradation were also enhanced. In a bacterial challenge with Yersinia ruckeri, dietary supplementation with GP significantly enhanced survival outcomes in treated groups compared to the CON group (P < 0.05). These results indicate that GP supplementation at 200-800 mg/kg promotes growth performance, strengthens intestinal health, modulates immunity, and enhances resistance to bacterial infections in channel catfish.

Body color is one of the most important traits in fish affecting species recognition, mate selection, and its economic value. Dissecting the genetic architecture underlying the body color diversity is important in tilapia. In this study, we successfully dissected the genetic architecture affecting black spot variation in two mapping populations of tilapia (a full-sib family: N = 103 a mixed population: N = 290) using ddRAD-seq-based GWAS technology. A major QTL interval for black spot trait on ChrLG3 (9.8–14.2 Mb) with a peak located at ChrLG3_11207231 was identified. The significant correlations (P < 0.001) between genotypes and color data were validated by applying a novel microsatellite marker (SSR-BC-1). A total of 14 genome-wide significant SNPs near or under the peak of the major QTL were located in exons or introns of nfib (6) and dennd4c (8). Furthermore, qRT-PCR analysis indicated both genes were differentially expressed in the skin and brain of black and red tilapia. Our study laid a foundation for exploring the genetic mechanism of body color variation and carrying out genetic improvement for color quality in tilapia.

In euryhaline fish frequently exposed to salinity shifts, epigenetic mechanisms are expected to play a crucial role in facilitating adaptation. Nile tilapia Oreochromis niloticus is recognized for its rapid growth and adaptability to low-salinity environments. The GIFT strain of the tilapia is suggested to be a good candidate for culture in brackish water. Recently, the mechanisms underlying salinity challenge in tilapia have received increasing attention. In this study, the dynamics of DNA methylation in the skin tissue of GIFT tilapia in response to high salinity stress were explored by integrating whole-genome bisulfite sequencing (WGBS) with published transcriptomic and genetic data. DNA methylation was enriched in heterochromatin and correlated positively with the density of transposable elements (TEs). A notable increase in CpG methylation level was detected, especially in the body of TEs, possibly due to the downregulated expression of DNA demethylases. Among the 10,514 differentially methylated regions (DMRs), 6346 showed hypermethylation, and 4168 displayed hypomethylation, with a marked prevalence on the chromosome LG3. Integration of methylation data with the skin transcriptome data unveiled a significant negative correlation (p < 0.05) between methylation levels in promoter regions and gene expression. Colocalization of differentially expressed genes (DEGs) and differentially methylated promoters (DMPs) identified 69 candidate genes. Additionally, 17 DMRs were overlapped with or near to the 24 SNPs on chromosome LG18:24,543,912 to 29,002,006 that significantly associated with salinity tolerance, highlighting candidate genes like mtcl1, nfatc4, pex19, kirrel1b, acot4, and pard3ab acting in adaption to high salinity. The methylation differences and expression changes of the candidate gene acot4 under high salinity stress were confirmed through BS-PCR and qRT-PCR. This investigation offers novel gene resources for further functional study on tilapia's adaptation to salinity changes from the genetic and epigenetic perspectives.

During wintering, red tilapia may develop variable black spots on their bodies, significantly reducing their market value. Understanding the mechanisms driving this phenomenon is essential for molecular improvements in body color. In this study, we investigated chromatin accessibility landscapes in the eyes of red tilapia with two distinct phenotypes (normal pure red and black spot) under wintering stress using ATAC-seq and RNA-seq analyses. We observed that approximately 32.7

Epigenetic regulation plays an important role in response to biotic stressors in fish. Streptococcus agalactiae (S. agalactiae) disease is one of the major threats to the tilapia aquaculture industry. However, the mechanism of epigenetic regulation involved in the immune response of tilapia against S. agalactiae infection is still unclear. In this study, genome-wide chromatin accessibility profiles in spleen of GIFT strain of nile tilapia (Oreochromis niloticus) in response to S. agalactiae infection were evaluated through ATAC-seq and RNA-seq. We identified 8161 differentially chromatin accessible regions (DARs) associated with 3642 genes in spleen in response to S. agalactiae infection. Compared with the susceptible group, the number of down-regulated DARs in the core promoter region of the resistant group was 8.33-fold more than that of the up-regulated DARs. The DAR-associated genes were enriched in pathways related to innate and adaptive immune responses, including autophagy, C-type lectin receptor signaling pathway, Toll-like receptor signaling pathway, Notch signaling pathway, and endocytosis. Thirteen Erythroblast Transformation Specific (ETS) family transcription factors (TFs), six differentially expressed TFs (ETV4, ETS1, ETV2, BHLHE40, ETV1, and CTCF) and 551 differential target genes for the ETS family were identified. The target genes are closely related to immune pathways such as lysosomal function, endocytosis, proteasome activity, peroxisome action, and ferroptosis. In particular, we found three ETS family target genes (birc2, melk, and usp4) closely related to disease resistance in GIFT tilapia. This study first explored the genome-wide chromatin accessibility profiles of spleen tissue of GIFT tilapia in response to S. agalactiae infection, providing a new epigenetic perspective for understanding the immune response of tilapia to S. agalactiae infection.

Streptococcus agalactiae (GBS) poses significant threats to various marine and freshwater fish species. Litsea cubeba oil (LCO) exhibits pharmacological activities including anti-inflammatory, appetite stimulation, and protection of intestinal barrier function. In this study, we examined the growth performance, antioxidant activities, and intestinal immune function of GIFT strain of Nile tilapia after 4 and 8 weeks of dietary supplementation of 0.5 %, 1.0 %, and 1.5 % LCO following GBS infection by using morphological methods, RNAseq and metagenomics analysis. We found LCO can significantly enhance the growth of tilapia, optimize feed utilization, markedly reduce triglycerides and total cholesterol, and enhance the proportion of crude protein and crude fat in tilapia flesh. Dietary supplementation of LCO has also significantly increased the number of villi and basement membrane thickness in the hindgut, as well as reducing villus fragmentation caused by GBS infection. Furthermore, LCO has significantly enhanced antioxidant enzyme activity and malondialdehyde levels in tilapia serum. A multitude of differentially expressed genes (DEGs) were enriched in immune-related pathways, including the intestinal immune network for IgA production, neuroactive ligand-receptor interaction, and calcium signaling pathway (P < 0.05). LCO influenced gut microbial diversity and community structure in tilapia. With the increase in LCO concentration, it helps to maintain the homeostasis of the intestinal microbial structure, which is destroyed by GBS infection. The relative abundance of Streptococcus and Arthrobacter was positively correlated with the expression values of genes TLR18, ACOD1, IL-1 beta, and hepcidin (P < 0.05). These findings indicate that dietary supplementation of LCO can enhance the growth, antioxidant capacity, and intestinal immunity of tilapia. LCO has the potential to be used as an effective candidate for improving growth and preventing GBS infections in tilapia.

Epigenetic mechanism plays a pivotal role in the immune responses of fish. Streptococcus agalactiae (SA) infection is a significant challenge to tilapia aquaculture. DNA methylation involved in immune responses in tilapia against SA is unclear. Here, by using a QTLseq strategy integrated with whole-genome bisulfite sequencing-based DNA methylation analysis (methyl-QTLseq) and RNA sequencing (RNA-seq), we identified 3608 differentially methylated regions (DMRs) and 4355 differentially expressed genes (DEGs) in the spleen of Nile tilapia Oreochromis niloticus. Compared to the susceptible group, the up-regulated DMRs (2449) were approximately twice as many as the down-regulated DMRs (1159). Compared to the susceptible group, lower methylation levels for CpG, CHG and CHH in TEs and for CHG and CHH in genes and significant decreased expression for 8 of the 11 DNA methyltransferase genes in the resistant group were detected. 46 DEGs with differentially methylated promoter regions (DMPs) were significantly enriched in immune processes such as T cell differentiation and adaptive immunity. We detected 4 methyl-QTLs located on LG8:5332501-5,336,400, LG14:2307301-2,353,500, LG16:16889101-16,903,500, and LG22:25238401-2,536,880 across the tilapia genome. The methyl-QTL region located within the chromosome LG22:25238401-25,368,800 contains the most DMRs (91) and DMGs (7). Interestingly, most of the annotated genes that located within or under the peak of the methyl-QTL interval belong to the HOX protein family including hoxa1, hoxa2, hoxa4a and hoxa5a. Bisulfite sequencing PCR and expression analysis indicated that DNA methylation in the promoter regions of hoxa4a, lcp2a, and ccr9a regulated gene expression in spleen in response to SA infection. Overall, our study provides epigenetics evidences involving in immune responses against SA infection in tilapia.

The genetic architecture of the resistance trait to Streptococcus agalactiae (GBS) infection in tilapia is unclear. In this study, we explored the QTLs associated with resistance to GBS infection in the GIFT strain of Nile tilapia (Oreochromis niloticus) by QTLseq and Methyl-QTLseq. 5,401,671 SNP loci were observed between extreme resistant and susceptible tilapia populations, however, did not reveal genome-wide significant QTL regions by QTLseq analysis. By using Methyl-QTLseq, we detected 5224 differentially methylated regions (DMRs) in the spleen, 1800 DMRs in the brain, and 18 DMRs in the liver of extreme resistant and susceptible tilapia populations. Using a sliding window approach, three significant methyl-QTLs were identified in the spleen on the genome region LG14: 2346001-2,351,600, LG16: 16890001-16,902,800, and LG22: 25323601-25,349,600, and two methyl-QTLs in the brain on LG14: 2347201-2,351,600 and LG22: 25323601-25,349,600. No methyl-QTLs were found in the liver. Several HOX family genes were observed under the methyl-QTL region of LG22. The differential methylation and expression level of the candidate lcp2a gene were validated and its core promoter region was determined in 450 bp to 150 bp upstream of the TSS that overlapped with the DMR region. In conclusion, our study suggests that the total heritability explained by DNA polymorphisms cannot explain the differences in resistance to GBS infection in tilapia, while DNA methylation may compensate for loss of missing heritability.

Aquaculture is an important sector for ensuring global food security. Due to the scarcity of freshwater available for expanding aquaculture, the development of omnivorous fish species and varieties that can tolerate high salinity will enhance fish production. Some tilapia species are good candidates for aquaculture in brackish and seawater because they can grow in high salinity. Among tilapia species, Oreochromis mossambicus, Oreochromis aureus, Oreochromis spilurus, Oreochromis urolepis hornorum, Sarotherodon galilaeus and Coptodon zillii are the most salinity-tolerant. Hybrids derived from salinity-tolerant tilapia species are tolerant to a certain level of salinity. They have been used in aquaculture production in brackish water and full seawater. Conventional selective breeding has been applied to increase the growth rate of salinity-tolerant tilapias. However, their growth rate is lower than that of the freshwater Oreochromis niloticus. Recently, many genomic resources and tools have been developed for salinity-tolerant tilapia. Quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) for important economic traits, including salinity tolerance and other desired traits, have been carried out and applied in molecular breeding for superior salinity-tolerant tilapia lines. In this review, we systematically analysed tilapia species that can be cultured in brackish and saltwater. We summarized previous works in conventional breeding and molecular breeding for salinity-tolerant tilapia. We pointed out a few known and potential challenges in the selective breeding and culture of salinity-tolerant tilapia. Due to the rapid advances in molecular and other disruptive technologies, we are optimistic that novel breeding approaches will significantly increase the production salinity-tolerant tilapia.

Salinity tolerance is a complex trait of ecological and economic importance in tilapia aquaculture. To further dissect the genetic architecture underlying this trait, we performed a genome-wide association study (GWAS) using ddRAD-seq in an F 1 tilapia population of GIFT tilapia, which is derived from selective breeding. Unlike previous studies localized to similar to 23 Mb on chrLG18, we identified 11 novel genome-wide significant SNPs spanning a 4.6 Mb region (24,593,966 to 29,240,173 bp) on chrLG18 associated with salinity tolerance. GO enrichment analysis of the genes within this QTL region on chrLG18 showed significant enrichment of genes involved in fatty acid metabolism. The significant associations with salinity tolerance for the two missense mutations, LG18_25,305,119 (c.C388T) and LG18_25,305,122 (c.A391G), in the slc25a24l gene have been confirmed by Sanger sequencing. Individuals homozygotes for the T allele of LG18_25,305,119 and G allele of LG18_25,305,122 demonstrated over 2 -fold longer average survival times under high salinity challenge compared to the individuals with disadvantageous genotypes. The mutated 131th amino acid (I/V) in SLC25A24L corresponding to the location of the nonsynonymous SNP LG18_25,305,122 showed a strong association with habitat salinity differences when comparing orthologs between freshwater and marine fish species. Our findings provide novel insights into QTLs, candidate genes and mutations conferring enhanced osmoregulatory capacity in tilapia.

Pogostemon oil (PO) is a volatile oil extracted from Pogostemon cablin., a traditional Chinese medicinal plants. Clinical studies have confirmed that PO has broad-spectrum antibacterial activity, but the resistance and protective mechanism of PO against Streptococcus agalactiae (SA) infection in Genetically Improved Cultured Tilapia (GIFT, Oreochromis niloticus.) are still unclear. The purpose of our study was to verify the resistance of PO feed to SA infection and reveal the potential immune mechanism. These 252 Tilapias were randomly divided into three groups, each with three replicates. The control group CON was fed with basic diet; These experimental groups PO5 and PO15 were fed with 5 μ L / g, 15 μ L / g PO diet, respectively; After 28 days feeding, Tilapia were randomly selected from CON, PO5, and PO15 groups, respectively: 22 fishes in each group were intraperitoneally injected with PBS to produce NC, NP5, and NP15 groups; other 22 fishes in each group were intraperitoneally injected with SA to produce CK, SP5, and SP15 groups. Twelve hours after SA challenge, spleen tissues were collected to study the effect of PO feed resist SA infection in Tilapia by RNA-Seq. In addition, two independent acute SA challenge experiments were added to verify the protective ability of PO against SA infection. In the transcriptome results, co-expressed genes in MEgreen (divided by WGCNA) were enriched in immune-related pathways by KEGG analysis, including Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, MAPK signaling pathway, NOD-like receptor signaling pathway, and C-type lectin receptor signaling pathway. Cluster analysis of 166 shared DEGs responsible to SA infection identified two major clusters with almost opposite expression trends. il-1β (interleukin-1 beta), gpr84 (G protein-coupled receptor 84), and OXER1 (oxoeicosanoid receptor 1) belonged to both share DEGs and key co-expressed genes, were up-regulated by PO after SA infection. In the survival challenge of LD50 concentration of SA, 5μL / g (0.67% vs 53.33%, P < 0.01), 10 μL / g (0.67% vs 53.33%, P < 0.01), and 15 μL / g (33.33% vs 53.33%, P > 0.05) PO feed groups decreased Tilapia mortality compared to basic diet group. In the challenge of SA concentration 10 times higher than LD50, 15 μL / g PO feed (55% vs 95%, P < 0.05) reduced mortality compared to basic diet group, and 5 μL / g PO feed significantly prolonged the median survival time of 1 day. In general, 5–15 μL / g PO feeds improved the resistance of Tilapia to SA infection and reduced the mortality of Tilapia. The results of RNA-Seq provide data support for the molecular mechanism of PO feeds regulating the immune response of Tilapia to SA. Collectively, PO may have the potential to be developed as a dietary supplementation for preventing and treating SA infections.